Brachybacterium endophyticum (KCTC 49087, CGMCC 1.16391, M1HQ-2)

Name: Brachybacterium endophyticum (KCTC 49087, CGMCC 1.16391, M1HQ-2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159799

Type strain

Strain Designation M1HQ-2

Culture col. no. KCTC 49087 CGMCC 1.16391 M1HQ-2 JCM 33403

NCBI tax ID(s) 2182385

Special Collections JCM KCTC Literature strains

History KCTC <- Li Tuo, Zunyi Medical Univ. JCM <-- CGMCC 1.16391 <-- L. Tuo; Zunyi Med. Univ., China; M1HQ-2.

Links

Brachybacterium endophyticum M1HQ-2 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from from a surface-sterilized bark of Scutellaria baicalensis Georgi.

Gram-positive coccus-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 287887

KCTC 49087

@ref 20215

Last LPSN update 2026-05-29 08:44:17

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Dermabacteraceae

Genus Brachybacterium

Species Brachybacterium endophyticum

Full scientific name Brachybacterium endophyticum Tuo et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell shape	Confidence
66743	positive	0.7-1.5 µm	coccus-shaped
125439	positive			92.66

Colony morphology

@ref	Colony color	Colony shape	Medium used
66743	yellow	circular	Marine agar (MA)

Multicellular morphology

@ref	Forms multicellular complex	Complex name
66743		Substrate mycelia and aerial mycelia

Pigmentation

66743

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth
66743	ISP 2
66743	ISP 3
66743	ISP 4
66743	LB (Luria-Bertani) MEDIUM
66743	Marine agar (MA)
66743	Nutrient agar (Bacto)
66743	Reasoner's 2A agar (R2A)
66743	tryptic soy agar (TSA)

Culture temp

@ref	Growth	Type	Temperature (°C)
66743	positive	optimum	30
66743	negative	growth	42
66743	positive	growth	4-37
67770	positive	growth	28
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
66743	positive	optimum	8
66743		growth	4
66743		growth	12
66743	positive	growth	5-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
66743	aerobe
67771	aerobe
125439	obligate aerobe	96.649

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66743	NaCl	positive	growth	0-15 %(w/v)
66743	NaCl	positive	optimum	1-3 %(w/v)

Observation

@ref	Observation
66743	The cell-wall peptidoglycan contains meso-diaminopimelic acid as the diagnostic diamino acid.
66743	The predominant menaquinone is MK-7.
66743	The polar lipids comprise diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipid and an unidentified lipid.
67770	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66743	73918 ChEBI	3-O-methyl-D-glucose	+	oxidation
66743	18101 ChEBI	4-hydroxyphenylacetic acid	+	oxidation
66743	16411 ChEBI	acetic acid	+	oxidation
66743	13705 ChEBI	acetoacetate	+	oxidation
66743	17128 ChEBI	adipate	-	assimilation
66743	17925 ChEBI	alpha-D-glucose	+	oxidation
66743	17665 ChEBI	alpha-D-glucose 6-phosphate	+	oxidation
66743		alpha-hydroxybutyrate	+	oxidation
66743	73706 ChEBI	bromosuccinate	+	oxidation
66743		casein	+	hydrolysis
66743	17057 ChEBI	cellobiose	+	builds acid from
66743	17057 ChEBI	cellobiose	+	oxidation
66743	53258 ChEBI	citric acid	+	oxidation
66743	15570 ChEBI	D-alanine	+	oxidation
66743	17108 ChEBI	D-arabinose	+	builds acid from
66743	18333 ChEBI	D-arabitol	+	builds acid from
66743	18333 ChEBI	D-arabitol	+	oxidation
66743	29990 ChEBI	D-aspartate	+	oxidation
66743	15824 ChEBI	D-fructose	+	builds acid from
66743	15824 ChEBI	D-fructose	+	oxidation
66743	78697 ChEBI	D-fructose 6-phosphate	+	oxidation
66743	28847 ChEBI	D-fucose	+	oxidation
66743	12931 ChEBI	D-galactonate	+	oxidation
66743	15895 ChEBI	D-galactonic acid lactone	+	oxidation
66743	12936 ChEBI	D-galactose	+	oxidation
66743	30612 ChEBI	D-glucarate	+	oxidation
66743	8391 ChEBI	D-gluconate	+	oxidation
66743	17634 ChEBI	D-glucose	+	assimilation
66743	17634 ChEBI	D-glucose	+	builds acid from
66743	15748 ChEBI	D-glucuronate	+	oxidation
66743	16899 ChEBI	D-mannitol	+	assimilation
66743	16899 ChEBI	D-mannitol	+	oxidation
66743	16024 ChEBI	D-mannose	+	assimilation
66743	16024 ChEBI	D-mannose	+	builds acid from
66743	16024 ChEBI	D-mannose	+	oxidation
66743	16523 ChEBI	D-serine	-	oxidation
66743	17924 ChEBI	D-sorbitol	+	oxidation
66743	65327 ChEBI	D-xylose	+	builds acid from
66743	27689 ChEBI	decanoate	-	assimilation
66743	23652 ChEBI	dextrin	+	oxidation
66743	17113 ChEBI	erythritol	+	builds acid from
66743	4853 ChEBI	esculin	+	builds acid from
66743	15740 ChEBI	formate	+	oxidation
66743	24175 ChEBI	galacturonate	+	oxidation
66743	16865 ChEBI	gamma-aminobutyric acid	+	oxidation
66743	5291 ChEBI	gelatin	+	hydrolysis
66743	5291 ChEBI	gelatin	+	oxidation
66743	28066 ChEBI	gentiobiose	+	oxidation
66743	17234 ChEBI	glucose	+	fermentation
66743	32323 ChEBI	glucuronamide	+	oxidation
66743	17859 ChEBI	glutaric acid	+	oxidation
66743	17754 ChEBI	glycerol	+	builds acid from
66743	17754 ChEBI	glycerol	+	oxidation
66743	70744 ChEBI	glycine-proline	+	oxidation
66743	17596 ChEBI	inosine	+	oxidation
66743	30849 ChEBI	L-arabinose	+	assimilation
66743	30849 ChEBI	L-arabinose	+	builds acid from
66743	16467 ChEBI	L-arginine	+	oxidation
66743	29991 ChEBI	L-aspartate	+	oxidation
66743	18287 ChEBI	L-fucose	-	oxidation
66743	29985 ChEBI	L-glutamate	+	oxidation
66743	15971 ChEBI	L-histidine	+	oxidation
66743	18183 ChEBI	L-pyroglutamic acid	+	oxidation
66743	62345 ChEBI	L-rhamnose	+	builds acid from
66743	62345 ChEBI	L-rhamnose	+	oxidation
66743	17115 ChEBI	L-serine	+	oxidation
66743	24996 ChEBI	lactate	+	oxidation
66743	17716 ChEBI	lactose	+	oxidation
66743	25115 ChEBI	malate	-	assimilation
66743	25115 ChEBI	malate	+	oxidation
66743	17306 ChEBI	maltose	+	assimilation
66743	17306 ChEBI	maltose	+	builds acid from
66743	17306 ChEBI	maltose	+	oxidation
66743	28053 ChEBI	melibiose	+	oxidation
66743	37657 ChEBI	methyl D-glucoside	+	oxidation
66743	51850 ChEBI	methyl pyruvate	+	oxidation
66743	17268 ChEBI	myo-inositol	+	builds acid from
66743	17268 ChEBI	myo-inositol	+	oxidation
66743	63154 ChEBI	N-acetyl-beta-D-mannosamine	+	oxidation
66743	28800 ChEBI	N-acetylgalactosamine	+	oxidation
66743	59640 ChEBI	N-acetylglucosamine	+	assimilation
66743	59640 ChEBI	N-acetylglucosamine	+	oxidation
66743	35418 ChEBI	n-acetylneuraminate	+	oxidation
66743	17309 ChEBI	pectin	+	oxidation
66743	18401 ChEBI	phenylacetate	-	assimilation
66743	32032 ChEBI	potassium gluconate	+	assimilation
66743	17272 ChEBI	propionate	+	oxidation
66743	26490 ChEBI	quinate	+	oxidation
66743	16634 ChEBI	raffinose	+	oxidation
66743	17814 ChEBI	salicin	+	oxidation
66743	53258 ChEBI	sodium citrate	-	assimilation
66743	17164 ChEBI	stachyose	+	oxidation
66743	28017 ChEBI	starch	-	hydrolysis
66743	17992 ChEBI	sucrose	+	builds acid from
66743	17992 ChEBI	sucrose	+	oxidation
66743	27082 ChEBI	trehalose	+	oxidation
66743	32528 ChEBI	turanose	+	builds acid from
66743	32528 ChEBI	turanose	+	oxidation
66743	53424 ChEBI	tween 20	-	hydrolysis
66743	53423 ChEBI	tween 40	+	hydrolysis
66743	53423 ChEBI	tween 40	+	oxidation
66743	53426 ChEBI	tween 80	-	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite
66743		1 % sodium lactate
66743	161680	aztreonam
66743	71321	fusidate
66743	32735	guanidinium chloride
66743	6472	lincomycin
66743	48607	lithium chloride
66743	50694	minocycline
66743	100147	nalidixic acid
66743	75273	niaproof
66743	75248	potassium tellurite
66743	29673	rifamycin sv
66743	75229	sodium bromate
66743	64103	sodium butyrate
66743	75198	tetrazolium blue
66743	75193	tetrazolium violet
66743	45735	troleandomycin
66743	28001	vancomycin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
66743	16136 ChEBI	hydrogen sulfide

Metabolite tests

@ref	Chebi-ID	Metabolite	Methylred-test
66743	17234 ChEBI	glucose	+

Enzymes

@ref	Value	Activity	Ec
66743	acid phosphatase	+	3.1.3.2
66743	alkaline phosphatase	+	3.1.3.1
66743	alpha-chymotrypsin	-	3.4.21.1
66743	alpha-fucosidase	-	3.2.1.51
66743	alpha-galactosidase	-	3.2.1.22
66743	alpha-glucosidase	+	3.2.1.20
66743	beta-galactosidase	+	3.2.1.23
66743	beta-glucosidase	+	3.2.1.21
66743	beta-glucuronidase	+	3.2.1.31
66743	beta-mannosidase	+	3.2.1.25
66743	catalase	+	1.11.1.6
66743	cystine arylamidase	+	3.4.11.3
66743	cytochrome oxidase	-	1.9.3.1
66743	esterase (C 4)	+
66743	esterase Lipase (C 8)	+
66743	leucine arylamidase	+	3.4.11.1
66743	lipase (C 14)	-
66743	N-acetyl-beta-glucosaminidase	+	3.2.1.52
66743	naphthol-AS-BI-phosphohydrolase	+
66743	nitrate reductase	-	1.7.99.4
66743	trypsin	-	3.4.21.4
66743	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

66743

Fatty acid	Percentage
C15:0 anteiso	69.4
C17:0 anteiso	13.9
C16:0 iso	9.4
C15:0 iso	3
C14:0 iso	2.7
C14:0	1
C16:0	0.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body-Site	#Plant	#Bark
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Engineered	#Treatment	#Sterilized (Desinfected)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
66743	from a surface-sterilized bark of Scutellaria baicalensis Georgi	Scutellaria baicalensis	Guizhou	China	CHN	Asia	27.3819	107.7 27.3819/107.7	M1 media	per litre of distilled water: 0.25 g yeast extract, 0.5 g K2HPO4, 20.0 g agar; pH 7.2	2-4 weeks	28	The plant samples were washed and surface-sterilized. After drying in the hood, the surface-sterilized samples were ground into powder by using a micromill and spread onto M1 medium. The isolate was transferred and streaked onto International Streptomyces Project (ISP) 2 agar until pure strains were obtained.
67770	Surface-sterilized bark of Scutellaria baicalensis Georgi from Guizhou	Scutellaria baicalensis		China	CHN	Asia
67771	From medical plant(Scutellaria baicallensis Georgi), forest(N27Â°22'55"E107Â°42'3")	Scutellaria baicallensis		China	CHN	Asia	27.3819	107.701 27.3819/107.701

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM313058v1 assembly for Brachybacterium endophyticum M1HQ-2	contig	GCA_003130585	2182385.3	2837086405	2182385	66.93

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66743	Brachybacterium endophyticum strain M1HQ-2 16S ribosomal RNA gene, partial sequence	MH289757	1481		2182385

GC content

@ref	GC-content (mol%)	Method
67770	71	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM313058v1 assembly for Brachybacterium endophyticum M1HQ-2
NCBI: GCA_003130585

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	positive	92.66	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.65	no
125439	motility	BacteriaNetⓘ	no	73.84	no
125439	spore_formation	BacteriaNetⓘ	no	82.59	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Brachybacterium subflavum sp. nov., a novel actinobacterium isolated from the foregut of grass carp.	Ming H, Cheng LJ, Yi BF, Xia TT, Niu MM, Zhao ZY, Liu BB, Nie GX, Cui CX	Int J Syst Evol Microbiol	10.1099/ijsem.0.004839	2021
Phylogeny	Brachybacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from bark of Scutellaria baicalensis Georgi.	Tuo L, Yan XR, Li FN, Bao YX, Shi HC, Li HY, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003032	2018

References

#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66743	Li Tuo, Xiao-Rui Yan, Fei-Na Li, Yu-Xin Bao, Hui-Chang Shi, Hong-Ying Li and Cheng-Hang Sun: Brachybacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from bark of Scutellaria baicalensis Georgi. IJSEM 68: 3563 - 3568 2018 ( DOI 10.1099/ijsem.0.003032 , PubMed 30230442 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Brachybacterium endophyticum (KCTC 49087, CGMCC 1.16391, M1HQ-2)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003130585

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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